Class of Multiple Sequence Alignment Algorithm Affects Genomic Analysis

Identification of innate immunity elicitors using molecular signatures of natural selection

(2012) H. C. McCann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring the distance between multiple sequence alignments

(2011) B. P. Blackburne et al.   BIOINFORMATICS

High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes

(2011) P. Markova-Raina et al.   GENOME RESEARCH

Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution

(2011) S. Fujii et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring speciation and extinction processes from extant species data

(2011) T. Stadler   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Positive Selection Differs between Protein Secondary Structure Elements in Drosophila

(2010) Kate E. Ridout et al.   Genome Biology and Evolution

The Effect of Insertions, Deletions, and Alignment Errors on the Branch-Site Test of Positive Selection

(2010) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rfam: Wikipedia, clans and the "decimal" release

(2010) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Human-Specific Evolution and Adaptation Led to Major Qualitative Differences in the Variable Receptors of Human and Chimpanzee Natural Killer Cells

(2010) Laurent Abi-Rached et al.   PLoS Genetics

Phylogenetic assessment of alignments reveals neglected tree signal in gaps

(2010) Christophe Dessimoz et al.   GENOME BIOLOGY

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integration of evolutionary and desolvation energy analysis identifies functional sites in a plant immunity protein

(2009) M. Casasoli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment

(2008) Amarendran R Subramanian et al.   Algorithms for Molecular Biology

StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees

(2008) Ádám Novák et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees

(2008) Anne Kupczok et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Alignment Uncertainty and Genomic Analysis

(2008) K. M. Wong et al.   SCIENCE

Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis

(2008) A. Loytynoja et al.   SCIENCE

Patterns of Positive Selection in Six Mammalian Genomes

(2008) Carolin Kosiol et al.   PLoS Genetics